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NM_002900.3(RBP3):c.1682_1686dup (p.Thr563fs) AND Retinitis pigmentosa 66

Germline classification:
Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:
Jan 3, 2022
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV001376430.2

Allele description [Variation Report for NM_002900.3(RBP3):c.1682_1686dup (p.Thr563fs)]

NM_002900.3(RBP3):c.1682_1686dup (p.Thr563fs)

Gene:
RBP3:retinol binding protein 3 [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
10q11.22
Genomic location:
Preferred name:
NM_002900.3(RBP3):c.1682_1686dup (p.Thr563fs)
HGVS:
  • NC_000010.11:g.47350166_47350170dup
  • NG_029718.1:g.6796_6800dup
  • NM_002900.3:c.1682_1686dupMANE SELECT
  • NP_002891.1:p.Thr563fs
  • NC_000010.10:g.48389191_48389192insGGCCC
  • NC_000010.10:g.48389192_48389196dup
  • NM_002900.2:c.1682_1686dup
Protein change:
T563fs
Links:
dbSNP: rs1555211286
NCBI 1000 Genomes Browser:
rs1555211286
Molecular consequence:
  • NM_002900.3:c.1682_1686dup - frameshift variant - [Sequence Ontology: SO:0001589]
Observations:
1

Condition(s)

Name:
Retinitis pigmentosa 66 (RP66)
Identifiers:
MONDO: MONDO:0014093; MedGen: C3715216; Orphanet: 791; OMIM: 615233

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001573566Ocular Genomics Institute, Massachusetts Eye and Ear
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Apr 8, 2021) 		germlineresearch

PubMed (1)
[See all records that cite this PMID]

SCV0020581853billion
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Jan 3, 2022) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot provided1not providedresearch, clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Ocular Genomics Institute, Massachusetts Eye and Ear, SCV001573566.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (1)

Description

The RBP3 c.1682_1686dup variant was identified in an individual with retinitis pigmentosa with a presumed recessive inheritance pattern. Through a review of available evidence we were able to apply the following criteria: PVS1, PM2. Based on this evidence we have classified this variant as Likely Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From 3billion, SCV002058185.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

Frameshift: predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant (PVS1_VS). It is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.000032, PM2_M). The variant has been reported to be associated with RBP3 related disorder (ClinVar ID: VCV001065743). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1not providednot provided1not providednot providednot provided

Last Updated: Feb 20, 2024